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In cryo-electron microscopy (EM), molecular structures are determined from large numbers of projection images of individual particles. To harness the full power of this single-molecule information, we use the Bayesian inference of EM…
In this paper, we propose an efficient parallelization strategy for boundary element method (BEM) solvers that perform the electromagnetic analysis of structures with lossy conductors. The proposed solver is accelerated with the adaptive…
In this paper, we demonstrate how GPU-accelerated BEM routines can be used in a simple black-box fashion to accelerate fast boundary element formulations based on Hierarchical Matrices (H-Matrices) with ACA (Adaptive Cross Approximation).…
We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a…
In the next decade, the demands for computing in large scientific experiments are expected to grow tremendously. During the same time period, CPU performance increases will be limited. At the CERN Large Hadron Collider (LHC), these two…
In this paper, we present a GPU-accelerated direct-sum boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral formulation is used to ensure the fast convergence of Krylov…
Graphics Processing Units (GPUs) are high performance co-processors originally intended to improve the use and quality of computer graphics applications. Once, researchers and practitioners noticed the potential of using GPU for general…
This work presents a novel three-dimensional Crack Element Method (CEM) designed to model transient dynamic crack propagation in quasi-brittle materials efficiently. CEM introduces an advanced element-splitting algorithm that enables…
Boundary element methods (BEM) reduce a partial differential equation in a domain to an integral equation on the domain's boundary. They are particularly attractive for solving problems on unbounded domains, but handling the dense matrices…
The structure and function of biological molecules are strongly influenced by the water and dissolved ions that surround them. This aqueous solution (solvent) exerts significant electrostatic forces in response to the biomolecule's…
As the need for computational power and efficiency rises, parallel systems become increasingly popular among various scientific fields. While multiple core-based architectures have been the center of attention for many years, the rapid…
We consider differential Lyapunov and Riccati equations, and generalized versions thereof. Such equations arise in many different areas and are especially important within the field of optimal control. In order to approximate their…
This work focuses on model preparation for electrostatic simulations of CAD designs to realize a rapid virtual prototyping concept. We present a boundary element method (BEM) allowing discontinuous fields between surfaces. The corresponding…
The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale…
We present a massively parallel, GPU-accelerated implementation of the Bethe-Salpeter equation (BSE) for the calculation of the vertical excitation energies (VEEs) and optical absorption spectra of condensed and molecular systems, starting…
For modern IC design, electromagnetic coupling among interconnect wires plays an increasingly important role in signoff analysis. The requirement of fast and accurate capacitance extraction is becoming more and more urgent.The critical step…
In recent years, high performance scientific computing on graphics processing units (GPUs) have gained widespread acceptance. These devices are designed to offer massively parallel threads for running code with general purpose. There are…
This paper discusses the potential of graphics processing units (GPUs) in high-dimensional optimization problems. A single GPU card with hundreds of arithmetic cores can be inserted in a personal computer and dramatically accelerates many…
The peridynamic theory brings advantages in dealing with discontinuities, dynamic loading, and non-locality. The integro-differential formulation of peridynamics poses challenges to numerical solutions of complicated and practical problems.…
In this paper, we present algorithms and implementations for the end-to-end GPU acceleration of matrix-free low-order-refined preconditioning of high-order finite element problems. The methods described here allow for the construction of…